[Mne_analysis] a junior question on mne_setup_source_space

Alexandre Gramfort alexandre.gramfort at telecom-paristech.fr
Mon Mar 24 13:38:56 EDT 2014
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hi Peng,

> Thank you Alex for the reply.
> 1. I suppose you meant freeview is not the optimal tool for visualizing
> source space of mne. However, I wish to check the source space by
> visualisation before I move on to source reconstructions. I tried
> mne_analyze instead of freeview:

a source space contains the indices of the vertices used in the surface
segmented by freesurfer.

See fig on the right in:

http://www.frontiersin.org/files/Articles/70133/fnins-07-00267-r2/image_m/fnins-07-00267-g003.jpg

in the recent paper on MNE-Python:

http://journal.frontiersin.org/Journal/10.3389/fnins.2013.00267/full

so if you want to check the source space I guess you want to check the
freesurfer segmentation.

> 1.1 It seemed to detect surfaces generated by freesurfer (such as inflated
> etc.) automatically, which I can load by <load surfaces...> in the menu; but
> not those surfaces generated by watershed, even after I copy them to the
> <surf> subfolder under the subject folder.

watershed is for the BEM not the source space.
you should be able to view them with freeview though.

> 1.2 I cannot load -src.fif either in mne_analyze. It complains 'Come on, It
> is not an MEG/EEG measurement file'...

yes it's not really meant to be visualized. I can send you script used
to make the figure on the frontiers paper if you want.

> 2. I tried the example in the script you provided (watershed), error
> happened while Decimating the dense tessellation...
>
> "/Applications/MNE-2.7.4-3378-MacOSX-x86_64/bin/mne_make_scalp_surfaces:
> line 125: -nojvm: command not found". I do have <mne_make_scalp_surfaces>
> file in the path. (Platform: MacOS10.9.2, macbook pro).

it's because mne_make_scalp_surfaces used matlab for decimation.
there is a python alternative.

Try

mne make_scalp_surfaces

if you have mne python installed correctly.

but it's just for visualization not computation.

> 3. If my data are MEG instead of EEG, do I still need to use this skin,
> skull, brain segmentations from watershed or mne_setup_source_space on brain
> surfaces is already sufficient?

you need the inner skull. This command should do the job:

mne_setup_forward_model --homog --surf --ico 4

then mne_do_forward_solution

see :

https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run_meg_tutorial.sh

for a full script.

maybe:

http://martinos.org/mne/dev/command_line_tutorial.html#command-line-tutorial

this can help too although it's not really up to date (but it should work)

> Thank you very much and sorry about so many questions...

no pb

Alex



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